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==ホモロジー検索等 | ==ホモロジー検索等== | ||
'''blast''' Sequence Similarity Search | '''blast''' Sequence Similarity Search | ||
'''blast+''' | '''blast+''' | ||
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'''EMBOSS''' [http://emboss.sourceforge.net/] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology | '''EMBOSS''' [http://emboss.sourceforge.net/] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology | ||
==マルチプルアラインメント== | ==マルチプルアラインメント== | ||
'''clustalw''' Multiple Sequence Alignment | '''clustalw''' Multiple Sequence Alignment | ||
'''clustalw2''' | '''clustalw2''' | ||
'''muscle''' [http://www.drive5.com/muscle/] Multiple Sequence Alignment faster and more accurate than clustalw | '''muscle''' [http://www.drive5.com/muscle/] Multiple Sequence Alignment faster and more accurate than clustalw | ||
'''mafft''' [http://mafft.cbrc.jp/alignment/software/] MAFFT is a multiple sequence alignment program | '''mafft''' [http://mafft.cbrc.jp/alignment/software/] MAFFT is a multiple sequence alignment program | ||
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'''Gblocks''' [http://molevol.cmima.csic.es/castresana/Gblocks.html] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences | '''Gblocks''' [http://molevol.cmima.csic.es/castresana/Gblocks.html] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences | ||
==アセンブラー== | |||
'''CAP3''' Multiple Sequence Alignment | |||
'''TGICL''' | |||
'''Phred''' [http://www.phrap.org/phredphrapconsed.html] The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base | |||
'''Phrap''' Phrap is a program for assembling shotgun DNA sequence data | |||
'''consed''' Assembly Editor | |||
==次世代シーケンサデータ解析用== | ==次世代シーケンサデータ解析用== | ||
'''samtools''' [http://samtools.sourceforge.net/] SAM Tools provide various utilities for manipulating alignments in the SAM format | '''samtools''' [http://samtools.sourceforge.net/] SAM Tools provide various utilities for manipulating alignments in the SAM format |
2014年11月25日 (火) 07:50時点における版
ホモロジー検索等
blast Sequence Similarity Search blast+ fasta
blat [1] BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more
遺伝子情報取得
dbget DBGET is an integrated database retrieval system for major biological databases
分子生物学用ソフトウェアパッケージ
EMBOSS [2] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology
マルチプルアラインメント
clustalw Multiple Sequence Alignment clustalw2
muscle [3] Multiple Sequence Alignment faster and more accurate than clustalw
mafft [4] MAFFT is a multiple sequence alignment program
t_coffee [5] Multiple sequence alignment package
Gblocks [6] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences
アセンブラー
CAP3 Multiple Sequence Alignment TGICL
Phred [7] The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base
Phrap Phrap is a program for assembling shotgun DNA sequence data
consed Assembly Editor
次世代シーケンサデータ解析用
samtools [8] SAM Tools provide various utilities for manipulating alignments in the SAM format
bwa [9] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence
soap [10] Short Oligonucleotide Analysis Package
abyss [11] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
allpaths-lg [12] The new short read genome assembler
bowtie [13] Bowtie is an ultrafast, memory-efficient short read aligner tophat [14] TopHat is a fast splice junction mapper for RNA-Seq reads cufflinks [15] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
trinityrnaseq [16] Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
velvet [17] Sequence assembler for very short reads
denovo2
遺伝子領域予測
genemark [18] A family of gene prediction programs
genscan [19] Gene prediction
glimmer [20] Glimmer is a system for finding genes in microbial DNA
モチーフ検索
hmmer [21] Biosequence analysis using profile HMM
meme [22] Multiple Em for Motif Elicitation
系統樹解析
mrbayes [23] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
njplot [24] NJplot is a tree drawing program
paup [25] Tools for inferring and interpreting phylogenetic trees
phylip [26] A package of programs for inferring phylogenies (evolutionary trees)
phyml [27] PhyML is a phylogeny software based on the maximum-likelihood principle
tree-puzzle [28] Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood
lastz
- インストール済みソフトウェア(その他)
Gene Spring (端末室 Windowsマシン上 所内のみ利用可) MATLAB (同上) MATLAB Distributed Computing Server
- 他一般ソフトウェア、プログラム言語
csh tcsh zsh bash perl ruby python gcc icc (Intel Compiler) mpicc